Hi Shilong, On Thu, Aug 18, 2011 at 5:55 AM, Shilong Fan <fanshil...@hotmail.com> wrote: > normaly you can do it in the pymol. In the main interface, on the left menu, > there is a:"A" button, click it, then looking for "Aliagn". Then you can do > it. > > But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine > any region you want to do superpose.
PyMOL can indeed perform alignments. It has three different methods and I'd like to take a second to clear up the differences. First, the "align" command (A > Align >) performs a sequence alignment followed by a few rounds of fitting throw away outliers to improve the fit. The "super" command is similar to align, but if you indicate "seq=0" then PyMOL will ignore the sequence. It then uses a dynamic programming strategy to find the best fit. Last, PyMOL also offers access to the structure-only "cealign" method as well. Of course, if you already know your paired atoms you can just use any of the 'fit' commands to do the fitting. Here are links to the PyMOLWiki pages for reference: * -- http://www.pymolwiki.org/index.php/Align * -- http://www.pymolwiki.org/index.php/Super * -- http://www.pymolwiki.org/index.php/Cealign * -- http://www.pymolwiki.org/index.php/Fit Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
